3D X-ray flat panel detector based cone beam imaging CT system provides an unprecedented advantage for high spatial resolution display of the 3D volume data due to its 3D isotropic spatial resolution. However, since the increase of the X-ray coverage along the rotation axis, the scatter correspondingly increases resulting in the decrease of the low contrast resolution as well as the non-uniformity artifacts across the reconstructed cross sectional image view. The use of the grid decreases of the primary X-ray beam intensity, which results in the noise increase in the reconstructed image. Furthermore, after the software based scatter correction which is usually conducted through the subtraction of the estimated scatter distribution 2D data from the corresponding original projection data in the linear space, the uniformity gets better at the cost of higher noise in the reconstructed image domain. That's why for the soft tissue, the CBCT can not provide comparable contrast to noise ratio (CNR) to conventional fan beam CT or multi-slice CT due to the higher scattering and less X-ray dose level.